The tree is created using UPGMA and distances shown are computed based on pairwise allelic differences (hamming distance). Missing genes are not included in the count.
The ambition with 1928’s outbreak analyses is to reproduce results from scientific studies and highlight the quality of the results generated by the 1928 platform.
In order to demonstrate the accuracy of outbreak analysis with the 1928 platform, a phylogenetic tree is created from an outbreak of Enterococcus faecium. The tree shown in the figure above is generated using the 1928 analysis platform.
In this analysis, 1928 reproduces results from the scientific paper Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network (pmid: 26759031) by Hayley J. Brodrick, Kathy E. Raven, Ewan M. Harrison, Beth Blane, Sandra Reuter, M. Estée Török, Julian Parkhill, Sharon J. Peacock.
The 1928 Enterococcus faecium cgMLST schema is created from 53 reference genomes giving the scheme 1315 core genes. All genes included in the schema are present in at least 95% of reference genomes.